On her second birthday, Molly became "lost in a storm", and fell into the clutches of Kotris. Kotris took Molly to his TARDIS and infused her with retro-genitor particles, then returned her home to her parents. (AUDIO: Tangled Web) The effect of the retro-genitor particles gave Molly unusually dark eyes. She was teased for her dark eyes when she was a child and when she first entered domestic service. However, this teasing ended when she began to punch the people who mocked her. (AUDIO: X and the Daleks)

Before the outbreak of World War I, she worked as a chambermaid for the Donaldson family in Eaton Place in London. She became friends with the Donaldsons' daughter Kitty, who viewed her as being the sister that she never had. When Kitty became a VAD in France, Molly did likewise as she knew that her mistress needed someone to protect her. After several months serving in France, Kitty contracted an infection from one of the soldiers whom she was treating. She was eventually killed by the renegade Time LordKotris and the Daleks. Molly met the Eighth Doctor in France, with whom she began to travel after they were chased across No Man's Land by the Daleks. (AUDIO: The Great War)

The first place the Doctor took Molly was Dunkirk in 1941. They were not there long before the Daleks appeared once more, chasing them across the town. They were also chased to London in 1972, and the planet Halalka. (AUDIO: Fugitives)

Shortly after leaving Halalka, Molly and the Doctor seemingly arrived on Skaro, where they discovered that the Daleks had become peaceful, after they caused the extinction of the Time Lords. However, it was later revealed that this was a simulation generated on their behalf. (AUDIO: Tangled Web)

The Doctor and Molly were directed to Srangor by the Time Lords, where Molly discovered that she had been implanted with retro-genitor particles. The effects of this were erased when Straxus — a younger version of Kotris — was killed, thus erasing Kotris and everything he accomplished from history.

She departed the TARDIS after it materialised in France during World War I. Molly realised that with Kotris having been erased from history, Kitty would still be alive and that she had to continue taking care of her as she promised. (AUDIO: X and the Daleks)

The Doctor and Molly travelled to the Orpheus, where Molly met Liv Chenka for the first time. Shortly after, the ship came under attack by the Eminence, and it began to possess the crew. After defeating the Eminence, Molly and the Doctor were joined on their travels by Liv. (AUDIO: Time's Horizon)

Molly, Liv and the Doctor's next stop was London in the 1970s, where Molly helped the Doctor to defeat the Master and the Eminence. After they were defeated, Molly stayed behind in 107 Baker Street and awaited the Doctor's return from Nixyce VII. One night she heard a knock at the door, and was kidnapped by Sally Armstrong and the Master. (AUDIO: Eyes of the Master)

The Master edited Molly's memories, replacing the Doctor with the Master, creating a sense of trust between them. (AUDIO: Rule of the Eminence) The Master took Molly to Heron's World, where she became part of the Master's experiment to pass some of her retro-genitor particles onto other humans. (AUDIO: The Death of Hope) The Master place her in her initial teleportation capsule hoping that he could the Eminence under his control. (AUDIO: Masterplan)

The Master used her to create the grand administrator Walter Vincent based on her father. Her singing annoyed the Master. Molly parted company from the Doctor after it was deemed she would be unsafe travelling with him, they parted ways as she was to be returned to her proper place in time by Narvin. (AUDIO: Rule of the Eminence)

In the new Dalek timeline, she was in Moscow, 1961 where she was known under the name Mary Carter Rastel ordered her to look after the Eighth Doctor. She didn't recognise him at first, but this was a deception. The Master wanted her to stabilise the timeline. She knew that something was wrong with time when the Daleks invaded Earth as she had known the future. (AUDIO: Master of the Daleks)

After the Dalek Time Controller took Liv and Molly to the Eye of Orion, she started to become ill. When the Doctor met up with her she started to feel better, and wanted the Doctor to stop the Daleks. She also tried to stop Anya. Her eyes turned dark for the last time, which allowed her to control the TARDIS. Because of the retro-genitor particle she was still linked with the Time Controller if either of them died they would both die. She scarificed her own life so that the Time Controller could die, and she became part of The Eminence. She used the Time Controller's link with the Time Vortex and sent the Eminence to the end of the universe. (AUDIO: Eye of Darkness)